Identification of Copy Number Variations and Selection Signatures in Wannan Spotted Pigs by Whole Genome Sequencing Data: A Preliminary Study

• Published in: Animals (Basel) Vol. 14; no. 10; p. 1419
• Main Authors: Zhang, Wei, Jiang, Yao, Ni, Zelan, Zhou, Mei, Liu, Linqing, Li, Xiaoyu, Su, Shiguang, Wang, Chonglong
• Format: Journal Article
• Language: English
• Published: Switzerland MDPI AG 01.05.2024
• Subjects: Animals; Asian wild boar; copy number variation; DNA sequencing; Fatty acids; Food supply; Genes; Genomes; Genomics; Germplasm; Hogs; Meat; Meat quality; Nucleotide sequencing; Nutrition; Pork industry; Requirements; selection signatures; Software; Wannan spotted pig; whole genome resequencing; China; United States > US; Asian wild boar; whole genome resequencing; copy number variation; Wannan spotted pig; selection signatures
• ISSN: 2076-2615; 2076-2615
• DOI: 10.3390/ani14101419

Copy number variation (CNV) is an important structural variation used to elucidate complex economic traits. In this study, we sequenced 25 Wannan spotted pigs (WSPs) to detect their CNVs and identify their selection signatures compared with those of 10 Asian wild boars. A total of 14,161 CNVs were detected in the WSPs, accounting for 0.72% of the porcine genome. The fixation index (Fst) was used to identify the selection signatures, and 195 CNVs with the top 1% of the Fst value were selected. Eighty genes were identified in the selected CNV regions. Functional GO and KEGG analyses revealed that the genes within these selected CNVs are associated with key traits such as reproduction ( and ), fatty acid composition ( , , , ), immune system ( ), ear size ( ), and feed efficiency ( ). The findings of this study contribute novel insights into the genetic CNVs underlying WSP characteristics and provide essential information for the protection and utilization of WSP populations.